#include <transport.h>

Inheritance diagram for ConvectionTransport:

Collaboration diagram for ConvectionTransport:

Classes
class	EqData

Public Member Functions
	ConvectionTransport (Mesh &init_mesh, const Input::Record &in_rec)

virtual	~ConvectionTransport ()

void	zero_time_step () override

void	update_solution () override

void	set_target_time (double target_time)

void	output_vector_gather ()

virtual void	output_data ()
	Write computed fields. More...

EqData *	get_data ()

OutputTime *	output_stream ()

double ***	get_concentration_matrix ()

void	get_par_info (int &el_4_loc, Distribution &el_ds)

int *	get_el_4_loc ()

int *	get_row_4_el ()

TimeIntegrationScheme	time_scheme ()
	Returns the time integration scheme of the equation. More...

Public Member Functions inherited from TransportBase
	TransportBase (Mesh &mesh, const Input::Record in_rec)

virtual	~TransportBase ()

virtual void	set_velocity_field (const MH_DofHandler &dh)

MassBalance *	mass_balance ()
	Sets pointer to data of other equations. TODO: there should be also passed the sigma parameter between dimensions. More...

unsigned int	n_substances ()
	Returns number of trnasported substances. More...

vector< string > &	substance_names ()
	Returns reference to the vector of substnace names. More...

virtual void	set_concentration_vector (Vec &vec)

Public Member Functions inherited from AdvectionProcessBase
	AdvectionProcessBase (Mesh &mesh, const Input::Record in_rec)

Public Member Functions inherited from EquationBase
	EquationBase ()

	EquationBase (Mesh &mesh, const Input::Record in_rec)

virtual	~EquationBase ()

virtual void	initialize ()
	Initialize fields. More...

virtual void	choose_next_time ()

virtual void	set_time_upper_constraint (double dt)

virtual void	set_time_lower_constraint (double dt)

TimeGovernor const &	time ()

virtual void	set_time_governor (TimeGovernor &time)

double	planned_time ()

double	solved_time ()

Mesh &	mesh ()

TimeMark::Type	mark_type ()

FieldSet &	data ()

virtual void	get_solution_vector (double *&vector, unsigned int &size)

virtual void	get_parallel_solution_vector (Vec &vector)

Public Member Functions inherited from EquationForMassBalance
virtual	~EquationForMassBalance ()

Private Member Functions
void	create_transport_matrix_mpi ()

void	make_transport_partitioning ()

void	set_initial_condition ()

void	read_concentration_sources ()

void	set_boundary_conditions ()

void	compute_concentration_sources (unsigned int sbi)

void	compute_concentration_sources_for_mass_balance (unsigned int sbi)

void	transport_matrix_step_mpi (double time_step)

void	alloc_transport_vectors ()

void	alloc_transport_structs_mpi ()

void	calc_fluxes (vector< vector< double > > &bcd_balance, vector< vector< double > > &bcd_plus_balance, vector< vector< double > > &bcd_minus_balance)

void	calc_elem_sources (vector< vector< double > > &mass, vector< vector< double > > &src_balance)

Private Attributes
EqData	data_

bool	is_convection_matrix_scaled

bool	need_time_rescaling

int	sub_problem

double *	sources_corr

Vec	v_sources_corr

double **	sources_density
	temporary arrays to store constant values of fields over time interval More...

double **	sources_conc

double **	sources_sigma

TimeMark::Type	target_mark_type
	TimeMark type for time marks denoting end of every time interval where transport matrix remains constant. More...

double	cfl_max_step

VecScatter	vconc_out_scatter

Mat	tm

double	transport_matrix_time

Vec *	vconc
	Concentration vectors for mobile phase. More...

double ***	conc
	Concentrations for phase, substance, element. More...

Vec *	vpconc

Vec *	bcvcorr

Vec *	vcumulative_corr

double **	cumulative_corr

Vec *	vconc_out

double ***	out_conc

Input::Record	output_rec
	Record with output specification. More...

OutputTime *	output_stream_

int *	row_4_el

int *	el_4_loc

Distribution *	el_ds

Friends
class	TransportOperatorSplitting

Additional Inherited Members
Public Types inherited from EquationForMassBalance
enum	TimeIntegrationScheme { none, explicit_euler, implicit_euler, crank_nicholson }

Static Public Attributes inherited from TransportBase
static Input::Type::Record	input_type_output_record

Protected Member Functions inherited from TransportBase
const RegionDB *	region_db ()
	Returns the region database. More...

Protected Attributes inherited from TransportBase
unsigned int	n_subst_
	Number of transported substances. More...

std::vector< string >	subst_names_
	Names of transported substances. More...

const MH_DofHandler *	mh_dh

MassBalance *	mass_balance_
	object for calculation and writing the mass balance to file. More...

Detailed Description

TODO:

doxy documentation
make separate method for changing time step (rescaling only), reassembly matrix only when data are changed
needs support from EqData to determine next change of the data for 1) transport matrix 2) source vector this allows us precisely choose interval where to fix timestep : field->next_change_time() - returns time jump or actual time in case of time dep. field Class that implements explicit finite volumes scheme with upwind. The timestep is given by CFL condition.

Definition at line 82 of file transport.h.

Constructor & Destructor Documentation

ConvectionTransport::ConvectionTransport	(	Mesh &	init_mesh,
		const Input::Record &	in_rec
	)

Constructor.

Definition at line 110 of file transport.cc.

ConvectionTransport::~ConvectionTransport ( )

virtual

TODO: destructor

Definition at line 216 of file transport.cc.

Member Function Documentation

void ConvectionTransport::alloc_transport_structs_mpi ( )

private

Definition at line 387 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::alloc_transport_vectors ( )

private

Definition at line 319 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::calc_elem_sources	(	vector< vector< double > > &	mass,
		vector< vector< double > > &	src_balance
	)

private

Implements the virtual method EquationForMassBalance::calc_elem_sources().

Definition at line 1345 of file transport.cc.

void ConvectionTransport::calc_fluxes	(	vector< vector< double > > &	bcd_balance,
		vector< vector< double > > &	bcd_plus_balance,
		vector< vector< double > > &	bcd_minus_balance
	)

private

Implements the virtual method EquationForMassBalance::calc_fluxes().

Definition at line 1304 of file transport.cc.

void ConvectionTransport::compute_concentration_sources ( unsigned int sbi)

private

Definition at line 486 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::compute_concentration_sources_for_mass_balance ( unsigned int sbi)

private

Definition at line 534 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::create_transport_matrix_mpi ( )

private

Assembly convection term part of the matrix and boundary matrix for application of boundary conditions.

Discretization of the convection term use explicit time scheme and finite volumes with full upwinding. We count on with exchange between dimensions and mixing on edges where more then two elements connect (can happen for 2D and 1D elements in 3D embedding space)

In order to get multiplication matrix for explicit transport one have to scale the convection part by the acctual time step and add time term, i. e. unit matrix (see. transport_matrix_step_mpi)

Updates CFL time step constrain.

Definition at line 800 of file transport.cc.

Here is the caller graph for this function:

double *** ConvectionTransport::get_concentration_matrix ( )

Definition at line 1279 of file transport.cc.

Here is the caller graph for this function:

EqData* ConvectionTransport::get_data ( )

inline

Getters.

Definition at line 184 of file transport.h.

Here is the caller graph for this function:

int * ConvectionTransport::get_el_4_loc ( )

Definition at line 1289 of file transport.cc.

void ConvectionTransport::get_par_info	(	int *&	el_4_loc,
		Distribution *&	el_ds
	)

Definition at line 1283 of file transport.cc.

Here is the caller graph for this function:

int * ConvectionTransport::get_row_4_el ( )

Definition at line 1293 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::make_transport_partitioning ( )

private

Definition at line 176 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::output_data ( void )

virtual

Write computed fields.

Reimplemented from EquationBase.

Definition at line 1377 of file transport.cc.

Here is the caller graph for this function:

OutputTime* ConvectionTransport::output_stream ( )

inline

Definition at line 186 of file transport.h.

Here is the caller graph for this function:

void ConvectionTransport::output_vector_gather ( void )

Communicate parallel concentration vectors into sequential output vector.

Definition at line 1254 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::read_concentration_sources ( )

private

void ConvectionTransport::set_boundary_conditions ( )

private

Definition at line 440 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::set_initial_condition ( )

private

Definition at line 297 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::set_target_time ( double target_time)

Use new flow field vector for construction of convection matrix. Updates CFL time step constrain. TODO: Just set the new velocity, postpone update till compute_one_step Set cross section of fractures from the Flow equation.

TODO: Make this and previous part of Transport interface in TransportBase. Set time interval which is considered as one time step by TransportOperatorSplitting. In particular the velocity field dosn't change over this interval.

Dependencies:

velocity, porosity -> matrix, source_vector matrix -> time_step

data_read_times -> time_step (not necessary if we won't stick to jump times) data -> source_vector time_step -> scaling

Definition at line 730 of file transport.cc.

Here is the caller graph for this function:

TimeIntegrationScheme ConvectionTransport::time_scheme ( )

inlinevirtual

Returns the time integration scheme of the equation.

Implements EquationForMassBalance.

Definition at line 193 of file transport.h.

void ConvectionTransport::transport_matrix_step_mpi ( double time_step)

private

Finish explicit transport matrix (time step scaling)

void ConvectionTransport::update_solution ( void )

overridevirtual

Calculates one time step of explicit transport.

Reimplemented from EquationBase.

Definition at line 600 of file transport.cc.

Here is the caller graph for this function:

void ConvectionTransport::zero_time_step ( )

overridevirtual

Initialize solution at zero time.

Reimplemented from EquationBase.

Definition at line 584 of file transport.cc.

Here is the caller graph for this function:

Friends And Related Function Documentation

friend class TransportOperatorSplitting

friend

Definition at line 309 of file transport.h.

Member Data Documentation

Vec* ConvectionTransport::bcvcorr

private

Definition at line 292 of file transport.h.

double ConvectionTransport::cfl_max_step

private

Definition at line 271 of file transport.h.

double*** ConvectionTransport::conc

private

Concentrations for phase, substance, element.

Definition at line 287 of file transport.h.

double** ConvectionTransport::cumulative_corr

private

Definition at line 294 of file transport.h.

EqData ConvectionTransport::data_

private

Parameters of the equation, some are shared with other implementations since EqData is derived from TransportBase::TransportEqData

Definition at line 248 of file transport.h.

int* ConvectionTransport::el_4_loc

private

Definition at line 306 of file transport.h.

Distribution* ConvectionTransport::el_ds

private

Definition at line 307 of file transport.h.

bool ConvectionTransport::is_convection_matrix_scaled

private

Indicates if we finished the matrix and add vector by scaling with timestep factor.

Definition at line 253 of file transport.h.

bool ConvectionTransport::need_time_rescaling

private

Definition at line 253 of file transport.h.

double*** ConvectionTransport::out_conc

private

Definition at line 297 of file transport.h.

Input::Record ConvectionTransport::output_rec

private

Record with output specification.

Definition at line 300 of file transport.h.

OutputTime* ConvectionTransport::output_stream_

private

Definition at line 302 of file transport.h.

int* ConvectionTransport::row_4_el

private

Definition at line 305 of file transport.h.

double ** ConvectionTransport::sources_conc

private

Definition at line 266 of file transport.h.

double* ConvectionTransport::sources_corr

private

Definition at line 261 of file transport.h.

double** ConvectionTransport::sources_density

private

temporary arrays to store constant values of fields over time interval

Definition at line 266 of file transport.h.

double ** ConvectionTransport::sources_sigma

private

Definition at line 266 of file transport.h.

int ConvectionTransport::sub_problem

private

Definition at line 256 of file transport.h.

TimeMark::Type ConvectionTransport::target_mark_type

private

TimeMark type for time marks denoting end of every time interval where transport matrix remains constant.

Definition at line 270 of file transport.h.

Mat ConvectionTransport::tm

private

Definition at line 277 of file transport.h.

double ConvectionTransport::transport_matrix_time

private

Time when the transport matrix was created. TODO: when we have our own classes for LA objects, we can use lazy dependence to check necessity for matrix update

Definition at line 282 of file transport.h.

Vec ConvectionTransport::v_sources_corr

private

Definition at line 262 of file transport.h.

Vec* ConvectionTransport::vconc

private

Concentration vectors for mobile phase.

Definition at line 285 of file transport.h.

Vec* ConvectionTransport::vconc_out

private

Definition at line 296 of file transport.h.

VecScatter ConvectionTransport::vconc_out_scatter

private

Definition at line 276 of file transport.h.

Vec* ConvectionTransport::vcumulative_corr

private

Definition at line 293 of file transport.h.

Vec* ConvectionTransport::vpconc

private

Definition at line 290 of file transport.h.

The documentation for this class was generated from the following files:

/home/jb/workspace/flow123d/src/transport/transport.h
/home/jb/workspace/flow123d/src/transport/transport.cc

Classes

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation